Assignment 4

setwd("C:/Users/arcaroadmin/Dropbox/2020 Bio697GA/Assignment 4")
SNPs <- read.table("23andMe_complete.txt", header = TRUE, sep = "\t")
library(ggplot2)
library(plotly)

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## Attaching package: 'plotly'

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## The following object is masked from 'package:stats':
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library(DT)

Exercise 1

Add title and labels for the x and y axis to Lab3 ex1. Color the bars blue

ggplot(SNPs, aes(x=chromosome)) + geom_bar(fill = "blue")

Exercise 2

To Lab3 ex3 add more defined x and y axis labels, add a title, Change the colors of the genotypes, so that the dinucleotides (e.g. AA) are one color, the mononucleotides (A) are another and D’s and I’s a third color. One way to do this is to specify the color of each genotype.

ggplot(SNPs, aes(x=chromosome, fill = genotype)) + geom_bar(color = "black") + xlab("Chromosomes") + ylab("Genotypes") + ggtitle("Lab 4, Exercise 2") + scale_fill_manual(values = c("black", "blue", "green", "green", "green", "green", "blue", "green", "green", "green", "red", "red", "red", "blue", "green", "green", "red", "red", "blue", "green"))

Exercise 3

From Lab3 ex5, make an output png file, then load the file into report using the RMarkdown or html format.

Lab 4, Exercise 3

Exercise 4

For Lab3 ex6 add more descriptive x and y axis labels, add a title, make the x-axis for each graph readable in your final report file.

ggplot(SNPs, aes(x=genotype, fill = chromosome)) + geom_bar(color = "black") + coord_polar() + facet_wrap(~chromosome) + xlab("Genotype broken down for each chromosome") + ylab("Genotype count") + ggtitle("Lab 4, Exercise 4")

Exercise 5

Turn Lab3 ex6 into an interactive graph using plotly

ggplotly(ggplot(SNPs, aes(x=genotype, fill = chromosome)) + geom_bar(color = "black") + facet_wrap(~chromosome) + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5), text = element_text(size=7)) + xlab("Genotype broken down for each chromosome") + ylab("Genotype count") + ggtitle("Lab 4, Exercise 4"))

Exercise 6

Make an interactive table of the SNPS found in on the Y chromosome from the 23andMe_complete data set

SNPs_Y <- subset(SNPs, chromosome == "Y")
datatable(SNPs_Y)

## Warning in instance$preRenderHook(instance): It seems your data is too big
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## rstudio.github.io/DT/server.html